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- PDB-3ehc: Crystal structure of a snoal-like polyketide cyclase (atu3018) fr... -

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Basic information

Entry
Database: PDB / ID: 3ehc
TitleCrystal structure of a snoal-like polyketide cyclase (atu3018) from agrobacterium tumefaciens str. c58 at 2.12 A resolution
ComponentsSnoaL-like polyketide cyclase
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologypolyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SnoaL-like polyketide cyclase (17741376) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SnoaL-like polyketide cyclase
B: SnoaL-like polyketide cyclase
C: SnoaL-like polyketide cyclase
D: SnoaL-like polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,73013
Polymers59,8704
Non-polymers8619
Water8,665481
1
A: SnoaL-like polyketide cyclase
B: SnoaL-like polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3196
Polymers29,9352
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-55 kcal/mol
Surface area12770 Å2
MethodPISA
2
C: SnoaL-like polyketide cyclase
D: SnoaL-like polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4117
Polymers29,9352
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-54 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.100, 114.060, 137.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 2 / Auth seq-ID: 3 - 127 / Label seq-ID: 3 - 127

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
SnoaL-like polyketide cyclase


Mass: 14967.464 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Gene: 17741376, AGR_L_3571, Atu3018 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7CRD4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5000M (NH4)2SO4, 12.0000% Glycerol, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97920, 0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.97921
30.979321
ReflectionResolution: 2.12→29.514 Å / Num. obs: 47190 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.63 % / Biso Wilson estimate: 34.929 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.77
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.12-2.20.5221.47178889327198.3
2.2-2.280.4551.6152427956197.2
2.28-2.390.3482.2180309388198.5
2.39-2.510.2662.9164198505198.6
2.51-2.670.194175099053198.6
2.67-2.880.1295.7174909046198.6
2.88-3.160.088.8167328618198.7
3.16-3.620.04414.4174398965198.6
3.62-4.550.02821.2172608867198.4
4.55-29.5140.02325.1175258911197.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.12→29.514 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.346 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.17
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (4). SULFATE (SO4) IONS AND GLYCEROL (GOL) MOLECULE FROM CRYSTALLIZATION SOLUTION WERE MODELED. (5). UNEXPLAINED ELECTRON DENSITIES NEAR RESIDUE 77 OF A/B/C/D CHAINS WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2392 5.1 %RANDOM
Rwork0.205 ---
obs0.207 47114 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.18 Å2 / Biso mean: 38.911 Å2 / Biso min: 16.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2---1.93 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.12→29.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 46 481 4664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224302
X-RAY DIFFRACTIONr_bond_other_d0.0030.022924
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9595829
X-RAY DIFFRACTIONr_angle_other_deg1.00937028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3025511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61523.361238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5715706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7041541
X-RAY DIFFRACTIONr_chiral_restr0.0890.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024846
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02987
X-RAY DIFFRACTIONr_nbd_refined0.1850.2748
X-RAY DIFFRACTIONr_nbd_other0.1950.22922
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22054
X-RAY DIFFRACTIONr_nbtor_other0.0840.22379
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2305
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.29
X-RAY DIFFRACTIONr_mcbond_it1.57532665
X-RAY DIFFRACTIONr_mcbond_other0.30731027
X-RAY DIFFRACTIONr_mcangle_it2.37954112
X-RAY DIFFRACTIONr_scbond_it4.28781878
X-RAY DIFFRACTIONr_scangle_it5.826111717
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A715TIGHT POSITIONAL0.060.05
2B715TIGHT POSITIONAL0.070.05
3C715TIGHT POSITIONAL0.060.05
4D715TIGHT POSITIONAL0.070.05
1A956MEDIUM POSITIONAL0.330.5
2B956MEDIUM POSITIONAL0.390.5
3C956MEDIUM POSITIONAL0.380.5
4D956MEDIUM POSITIONAL0.40.5
1A715TIGHT THERMAL0.160.5
2B715TIGHT THERMAL0.140.5
3C715TIGHT THERMAL0.150.5
4D715TIGHT THERMAL0.140.5
1A956MEDIUM THERMAL1.022
2B956MEDIUM THERMAL1.042
3C956MEDIUM THERMAL0.952
4D956MEDIUM THERMAL0.932
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 181 -
Rwork0.294 3251 -
all-3432 -
obs--99.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8114-0.5457-0.29572.4254-0.05540.85930.1098-0.06230.01580.0752-0.0068-0.0376-0.0257-0.0371-0.103-0.14260.0308-0.0388-0.1829-0.0313-0.1666-6.473724.1131-25.0319
21.89560.58621.71711.90541.4223.6311-0.0045-0.4091-0.32260.5516-0.03540.1020.351-0.30460.040.02920.01870.0018-0.05910.06-0.0943-11.86045.216-12.6472
31.23790.5478-0.30952.51880.04441.07220.06180.04650.0079-0.01130.0006-0.00160.03260.0479-0.0623-0.1671-0.0256-0.0727-0.19090.0396-0.13766.65617.331924.8114
42.0083-1.56141.42592.9432-1.88012.82420.29540.4192-0.3101-0.7031-0.20830.06440.50710.3889-0.08710.05070.0391-0.0713-0.0545-0.0426-0.06912.5504-11.408512.3817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 126
2X-RAY DIFFRACTION2B0 - 127
3X-RAY DIFFRACTION3C1 - 127
4X-RAY DIFFRACTION4D3 - 127

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